ExaBayes protocols

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ExaBayes specifications

Information


Unique identifier OMICS_10303
Name ExaBayes
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Parallelization MPI
Computer skills Advanced
Version 1.4.1
Stability Stable
Maintained No

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Publication for ExaBayes

ExaBayes in pipeline

2016
PMCID: 5055826
PMID: 27498812
DOI: 10.1093/aob/mcw151

[…] default settings and autoselected alignment strategy, which chose fft-ns-i for matk, ndhf and rbcl, and l-ins-i for rps16. we concatenated the alignments into a supermatrix and analysed this using exabayes v. 1.4.1 under default settings () to construct a posterior sample of trees, which we rooted on cornales. fig. 2. fig. 3. , we used our posterior sample of trees to run comparative analyses […]


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ExaBayes in publications

 (20)
PMCID: 5826337
PMID: 29515592
DOI: 10.3389/fimmu.2018.00304

[…] repeated with a larger set of 510 sequences representing s100s within this clade of the s100 family (data sheet s2, s4, s5, and s6 in supplementary material)., we constructed our bayesian tree using exabayes () using a single data partition, integrating over tree topologies, rates, and evolutionary models. we ran two replicate analyses, using three heated chains and a single cold chain per […]

PMCID: 5913673
PMID: 29385525
DOI: 10.1093/molbev/msy014

[…] the course of such an independent implementation effort. we believe that this strategy of comparing the results of independent implementations (e.g., phyml, iq-tree, raxml for maximum likelihood or exabayes, mrbayes, phylobayes for bayesian inference) represents a valuable approach to increasing our confidence regarding the correctness of these tools. in two independently developed tools […]

PMCID: 5768713
PMID: 29335414
DOI: 10.1038/s41467-017-02644-4

[…] (or 71,406 nucleotides). we estimated concatenated trees with both nucleotide and deduced protein sequences by using two maximum likelihood (ml) methods (raxml and iq-tree) and a bayesian approach (exabayes). the protein raxml analysis produced a well-resolved phylogeny (supplementary fig. ). other ml and bayesian analyses based on nucleotide or protein sequences resulted in nearly identical […]

PMCID: 5710718
DOI: 10.1093/gbe/evx233

[…] resulting trees were input for summary species tree analyses under two different approaches: astral-ii and mp-est. we then conducted concatenation analyses under ml (raxml and iq-tree) and bayesian (exabayes and phylobayes) criteria using the expanded data sets. to account for biases arising from the inclusion of fast-evolving sites (; ), we also selected the top 100 most conserved genes […]

PMCID: 5837689
PMID: 28945862
DOI: 10.1093/sysbio/syx070

[…] characters and number of partitions identified by partitionfinder are available in . resulting alignments were analyzed with bayesian, maximum likelihood, and coalescent methods using raxml, exabayes, astrid, astral-ii, and svdquartets as described in the methods section. bootstrap topologies stabilized in each alignment and partition combination within 150 replicates and all bayesian […]


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ExaBayes institution(s)
Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany

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